Maintenance updates (#550)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.12.1 → 24.3.0](psf/black@23.12.1...24.3.0) - [github.com/PyCQA/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0) - [github.com/nbQA-dev/nbQA: 1.7.1 → 1.8.5](nbQA-dev/nbQA@1.7.1...1.8.5) - [github.com/kynan/nbstripout: 0.6.1 → 0.7.1](kynan/nbstripout@0.6.1...0.7.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Maintenance updates * Update linter config * Downgrade actions * Add Pint shim back? * Skip OpenMM 7 and Python >3.10 * Pin to old pymbar * Pin to old pymbar * Skip macOS + OpenMM 7 There doesn't seem to be this combination of builds on 3.10+ --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
openforcefield · Apr 3, 2024 · 1105e66 · 1105e66
1 parent 02638dc
commit 1105e66
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -31,12 +31,12 @@ jobs:
           - ubuntu-latest
           - macOS-latest
         python-version:
-          - "3.9"
           - "3.10"
+          - "3.11"
+          - "3.12"
         pymbar-version:
           - "3.1"
         pydantic-version:
-          - "1"
           - "2"
         openmm-version:
           - "7"
@@ -45,8 +45,18 @@ jobs:
           - true
           - false
         exclude:
-          - python-version: "3.10"
+          - python-version: "3.11"
             openmm-version: "7"
+          - python-version: "3.12"
+            openmm-version: "7"
+          - os: "macOS-latest"
+            openmm-version: "7"
+          - python-version: "3.12"
+            openeye: true
+          - python-version: "3.11"
+            pymbar-version: "3.1"
+          - python-version: "3.12"
+            pymbar-version: "3.1"
 
     steps:
       - uses: actions/checkout@v4
@@ -71,11 +81,6 @@ jobs:
         env:
           SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
-      - name: Install Foyer
-        if: ${{ matrix.pydantic-version == 1 }}
-        shell: bash -l {0}
-        run: micromamba install foyer -c conda-forge
-
       - name: Install PASCAL Compiler (MacOS)
         if: startsWith(matrix.os, 'macOS')
         run: brew install fpc

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
 files: (^openff|^utilities|^integration-tests)
 repos:
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.3.0
   hooks:
   - id: black
   - id: black-jupyter
@@ -13,11 +13,11 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.1
+  rev: 1.8.5
   hooks:
     - id: nbqa-pyupgrade
       files: ^docs/tutorial
@@ -26,7 +26,7 @@ repos:
     - id: nbqa-isort
       files: ^docs/tutorial
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
+  rev: 0.7.1
   hooks:
     - id: nbstripout
       files: ^docs/tutorial
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -1,6 +1,5 @@
 name: evaluator-test-env
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
     # Base depends
@@ -14,11 +13,9 @@ dependencies:
   - pytest-randomly
   - nbval
   - requests-mock # For testing http requests.
-  # smirnoff-plugins =0.0.3
-  # Add back when MoSDeF supports pydantic v2
-  # foyer
+  - foyer
 
-    # Shims
+    # Shim
   - pint =0.20.1
 
     # Standard dependencies

diff --git a/integration-tests/paprika/run.py b/integration-tests/paprika/run.py
@@ -53,9 +53,11 @@ def main():
                 "BaseBuildSystem": (
                     "BuildSmirnoffSystem"
                     if isinstance(force_field_source, SmirnoffForceFieldSource)
-                    else "BuildTLeapSystem"
-                    if isinstance(force_field_source, TLeapForceFieldSource)
-                    else "BaseBuildSystem"
+                    else (
+                        "BuildTLeapSystem"
+                        if isinstance(force_field_source, TLeapForceFieldSource)
+                        else "BaseBuildSystem"
+                    )
                 )
             }
         )

diff --git a/openff/evaluator/_tests/test_attributes/test_attributes.py b/openff/evaluator/_tests/test_attributes/test_attributes.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.attributes
 """
+
 import json
 
 import pytest

diff --git a/openff/evaluator/_tests/test_client.py b/openff/evaluator/_tests/test_client.py
@@ -1,6 +1,7 @@
 """
 Units tests for the openff.evaluator.client module.
 """
+
 import tempfile
 
 import pytest

diff --git a/openff/evaluator/_tests/test_datasets/test_datasets.py b/openff/evaluator/_tests/test_datasets/test_datasets.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.datasets
 """
+
 import json
 
 import numpy

diff --git a/openff/evaluator/_tests/test_datasets/test_thermoml.py b/openff/evaluator/_tests/test_datasets/test_thermoml.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.datasets
 """
+
 import pytest
 from openff.units import unit
 

diff --git a/openff/evaluator/_tests/test_plugins.py b/openff/evaluator/_tests/test_plugins.py
@@ -1,6 +1,7 @@
 """
 Units tests for the openff.evaluator.plugins module.
 """
+
 import sys
 
 from openff.evaluator.layers import (

diff --git a/openff/evaluator/_tests/test_properties/test_properties.py b/openff/evaluator/_tests/test_properties/test_properties.py
@@ -2,6 +2,7 @@
 Units tests for the calculation schemas registered by
 `evaluator.properties`.
 """
+
 from collections import OrderedDict
 
 import pytest

diff --git a/openff/evaluator/_tests/test_protocols/test_coordinates.py b/openff/evaluator/_tests/test_protocols/test_coordinates.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff-evaluator.protocols.coordinates
 """
+
 import tempfile
 
 import pytest

diff --git a/openff/evaluator/_tests/test_protocols/test_forcefield.py b/openff/evaluator/_tests/test_protocols/test_forcefield.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.protocols.forcefield
 """
+
 import re
 import tempfile
 from os import path

diff --git a/openff/evaluator/_tests/test_protocols/test_miscellaneous.py b/openff/evaluator/_tests/test_protocols/test_miscellaneous.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.protocols.miscellaneous
 """
+
 import operator
 import random
 import tempfile

diff --git a/openff/evaluator/_tests/test_protocols/test_openmm.py b/openff/evaluator/_tests/test_protocols/test_openmm.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.protocols.openmm
 """
+
 import json
 import os
 import tempfile

diff --git a/openff/evaluator/_tests/test_protocols/test_storage_protocols.py b/openff/evaluator/_tests/test_protocols/test_storage_protocols.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.protocols.storage
 """
+
 import json
 import os
 import tempfile

diff --git a/openff/evaluator/_tests/test_server.py b/openff/evaluator/_tests/test_server.py
@@ -1,6 +1,7 @@
 """
 Units tests for the openff.evaluator.server module.
 """
+
 import tempfile
 from time import sleep
 

diff --git a/openff/evaluator/_tests/test_storage/test_local.py b/openff/evaluator/_tests/test_storage/test_local.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.storage.localfile
 """
+
 import os
 
 from openff.evaluator.storage import LocalFileStorage

diff --git a/openff/evaluator/_tests/test_storage/test_storage.py b/openff/evaluator/_tests/test_storage/test_storage.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.storage
 """
+
 import os
 import tempfile
 

diff --git a/openff/evaluator/_tests/test_substances.py b/openff/evaluator/_tests/test_substances.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.substances
 """
+
 import numpy as np
 import pytest
 

diff --git a/openff/evaluator/_tests/test_thermodynamics.py b/openff/evaluator/_tests/test_thermodynamics.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.thermodynamics
 """
+
 import pint
 import pytest
 from openff.units import unit

diff --git a/openff/evaluator/_tests/test_utils/test_execeptions.py b/openff/evaluator/_tests/test_utils/test_execeptions.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.exceptions
 """
+
 from openff.evaluator.utils import exceptions
 
 

diff --git a/openff/evaluator/_tests/test_utils/test_graph.py b/openff/evaluator/_tests/test_utils/test_graph.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.graph
 """
+
 import pytest
 
 from openff.evaluator.utils import graph

diff --git a/openff/evaluator/_tests/test_utils/test_observables.py b/openff/evaluator/_tests/test_utils/test_observables.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.observables
 """
+
 import json
 from typing import List, Tuple, Type, Union
 
@@ -995,10 +996,7 @@ def test_frame_from_openmm(pressure):
     if pressure is not None:
         expected_enthalpy = (
             13874.51498645249 * unit.kilojoule / unit.mole
-            + pressure
-            * 26.342326662784938
-            * unit.nanometer**3
-            * unit.avogadro_constant
+            + pressure * 26.342326662784938 * unit.nanometer**3 * unit.avogadro_constant
         )
         assert numpy.isclose(observable_frame["Enthalpy"].value[0], expected_enthalpy)
 
@@ -1084,11 +1082,7 @@ def test_frame_join():
                     {"Temperature": ObservableArray(value=numpy.ones(2) * unit.kelvin)}
                 ),
                 ObservableFrame(
-                    {
-                        "Volume": ObservableArray(
-                            value=numpy.ones(2) * unit.nanometer**3
-                        )
-                    }
+                    {"Volume": ObservableArray(value=numpy.ones(2) * unit.nanometer**3)}
                 ),
             ],
             pytest.raises(ValueError),

diff --git a/openff/evaluator/_tests/test_utils/test_packmol.py b/openff/evaluator/_tests/test_utils/test_packmol.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.packmol
 """
+
 import numpy as np
 import pytest
 from openff.units import unit

diff --git a/openff/evaluator/_tests/test_utils/test_serialization.py b/openff/evaluator/_tests/test_utils/test_serialization.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.serialization
 """
+
 import json
 from datetime import datetime
 from enum import Enum, IntEnum

diff --git a/openff/evaluator/_tests/test_utils/test_string.py b/openff/evaluator/_tests/test_utils/test_string.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.statistics
 """
+
 import tempfile
 from os import path
 

diff --git a/openff/evaluator/_tests/test_utils/test_tcp.py b/openff/evaluator/_tests/test_utils/test_tcp.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.tcp
 """
+
 from openff.evaluator.utils import tcp
 
 

diff --git a/openff/evaluator/_tests/test_utils/test_utils.py b/openff/evaluator/_tests/test_utils/test_utils.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.utils.exceptions
 """
+
 import os
 import tempfile
 

diff --git a/openff/evaluator/_tests/test_workflow/test_protocols.py b/openff/evaluator/_tests/test_workflow/test_protocols.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.workflow
 """
+
 import json
 import os
 import tempfile

diff --git a/openff/evaluator/_tests/test_workflow/test_workflow.py b/openff/evaluator/_tests/test_workflow/test_workflow.py
@@ -1,6 +1,7 @@
 """
 Units tests for openff.evaluator.layers.simulation
 """
+
 import math
 import os
 import tempfile

diff --git a/openff/evaluator/attributes/attributes.py b/openff/evaluator/attributes/attributes.py
@@ -2,6 +2,7 @@
 A collection of descriptors used to add meta data to
 object attributes.
 """
+
 import copy
 import inspect
 from collections.abc import Iterable, Mapping

diff --git a/openff/evaluator/attributes/typing.py b/openff/evaluator/attributes/typing.py
@@ -3,6 +3,7 @@
 typing into the framework, but rather to aid in statically verifying
 the protocols input and outputs align correctly.
 """
+
 import typing
 
 _supported_generic_types = {typing.Union}

diff --git a/openff/evaluator/backends/backends.py b/openff/evaluator/backends/backends.py
@@ -1,6 +1,7 @@
 """
 Defines the base API for the openff-evaluator task calculation backend.
 """
+
 import abc
 import re
 from enum import Enum

diff --git a/openff/evaluator/backends/dask.py b/openff/evaluator/backends/dask.py
@@ -1,6 +1,7 @@
 """
 A collection of openff-evaluator compute backends which use dask as the distribution engine.
 """
+
 import abc
 import importlib
 import logging

diff --git a/openff/evaluator/client/client.py b/openff/evaluator/client/client.py
@@ -1,6 +1,7 @@
 """
 Evaluator client side API.
 """
+
 import copy
 import json
 import logging